Small molecule inhibitors of influenza a rna-dependent rna polymerase

ABSTRACT

Antiviral compositions and methods are contemplated that are especially effective in the treatment and prevention of influenza A viruses. Also presented are cellular assays to identify small molecule compounds having antiviral properties, particularly as it relates to detection of influenza A RNA-dependent RNA polymerase activity in a mammalian cell independent of other influenza A components. Preferred assays allow for identification of viral replication inhibitors that do not disrupt normal cellular activity.

This application is a divisional of co-pending U.S. application Ser. No.14/103,267 filed Dec. 11, 2013, which is a divisional of applicationSer. No. 13/622,807, filed Sep. 19, 2012 and issued Jan. 21, 2014 asU.S. Pat. No. 8633198, which claims the benefit of priority to U.S.provisional application Ser. No. 61/536,691, filed Sep. 20, 2011. Theseapplications are each incorporated herein by reference in theirentirety.

FIELD OF THE INVENTION

The field of the invention is antiviral compounds and compositions.

BACKGROUND

Influenza A virus is a member of the orthomyxoviridae virus family of(−)-sense RNA viruses. The influenza A viral genome is composed of 8segments or chromosomes which encode 11 proteins^(l). During infection,the virus-encoded RNA-dependent RNA polymerase (RdRP) converts the(−)-stranded RNAs to (+) strand messenger RNAs and a set of full lengthcomplementary genomic RNAs (or cRNAs) which serve as templates forgenomic replication. Viral proteins expressed from the (+) strandmessenger RNAs go about the task of establishing infection andfacilitating viral replication, a process which ends in theamplification, assembly, and release of virus particles containing theinitial 8 (−) strand chromosomes which repeat the infectious cycle.

The processes associated with the transcription and replication of theinfluenza A genome have been under investigation for decades. All eightchromosomes of every influenza A strain (including H1N1 seasonal, H1N1“swine”, H3N2, and H5N1 “avian”) contain identical 5′ and nearlyidentical 3′ untranslated regions (UTRs) flanking the protein-codingportion of the sequence which otherwise encode distinct proteins.Experimental results demonstrate that the UTRs are recognized by RdRP asa promoter element and both components are critical for viral geneexpression and replication. Hence, the viral polymerase and its cognateUTR RNA ligand are thought to control the viral life cycle and arecritical targets for therapeutic intervention.

Despite such relatively detailed knowledge of viral replication,currently existing and clinically approved anti-influenza A therapeuticmolecules are restricted to small molecules that inhibit one of twotarget classes of viral coat proteins: Neuraminidase (NA) and Matrix 2(M2). NA belongs to a broad class of glycoside hydrolase enzymes (alsoknown as sialidases, as N- or O-linked neuraminic acids are collectivelycalled sialic acid) which cleave terminal sialic acid residues offvirions and host cell receptor proteins. During influenza A infection,NA activity is involved in viral transit through mucus secretions of therespiratory tract as well as for the biochemical separation/elution ofsecreted viruses from the infected cells serving as sites ofreplication, thereby enabling the infection of nearby healthy cells.Currently, oseltamivir (trade name Tamiflu®) and zanamivir (trade nameRelenza®) are two clinically approved medications for the treatment ofinfluenza infection through inhibition of NA while laninamivir (Inavir)and peramivir are currently in the late stages of clinical trials asnext-generation influenza NA inhibitors.

Unlike NA, influenza M2 is produced by the alternative splicing of themRNA encoding the viral structural protein, matrix (or M). In contrastto M which is one of the most highly abundant viral proteins ininfection and serves as a scaffold to which viral coat proteins andribonucleoprotein particles bind, M2 is present in minute amounts invirions and serves as an ion channel which enables viral uncoating andescape from endosomal compartments into the cellular cytoplasm, acritical step in replication. Clinically approved inhibitors of M2include amantadine (trade name Symmetrel®) and rimantadine (trade nameFlumadine®).

NA and M2 inhibitors serve as successful proof-of-concept small moleculeinhibitors of critical steps in the influenza virus infection cycle.Despite their early successes, however, use of both NA and M2 inhibitorshas met recent challenges in treating influenza infection through theemergence of viral variants exhibiting drug resistance. For example,evidence of viral resistance to Tamiflu has been documented in numerousclinically relevant influenza A isolates including the 2009 pandemic⁵,H3N2⁶, H5N1⁷, and seasonal H1N1⁸ where resistance existed in 99.6% ofcirculating isolates in 2008. Although influenza A resistance tozanamivir has yet to be reported, the report of an influenza B viralisolate resistant to this agent⁹ may indicate the possibility of futuremore prevalent resistance to this drug upon broad usage to treatinfluenza infections although the resistant virus described in thisstudy had acquired an additional compensatory mutation in the HA proteinwhich should reduce this possibility significantly. With regards to theM2 inhibitors, the Centers for Disease Control and Prevention indicatedthat nearly all circulating H3N2 and pandemic H1N1 virus isolates duringthe fall of 2009 were resistant to amantadines¹⁰.

Unfortunately, surveillance efforts have also identified the recentemergence of dual oseltamivir/adamantane resistant isolates¹¹ indicatingthe need for the discovery and utilization of additional small moleculeinhibitors targeting other critical viral targets. Thus, there is stilla need to provide new and/or improved antiviral drugs that interferewith viral replication, and especially RNA-virus replication.

SUMMARY OF THE INVENTION

The inventors have discovered various compositions and methods thatinterfere with the infectious life cycle of influenza A, and most likelywith viral replication. Moreover, the inventors have also discoveredcomponents and methods for a cellular assay to identify small moleculecompounds having antiviral properties. In especially preferred aspects,the assay allows for detection of influenza A RNA-dependent RNApolymerase activity in a mammalian cell independent of other influenza Acomponents, and allows for identification of inhibitors of viralreplication that do not disrupt normal cellular activity.

In another aspect of the inventive subject matter, selected compoundsare provided with antiviral properties. Particularly preferred compounds(A0435) were evaluated in an in vitro viral propagation system utilizingthree different influenza A strains representing two different serotypesof virus and found to inhibit all three viruses at low μM concentrationsand to prevent host cells from displaying virus-induced cytopathiceffects (CPE). Consistent with these results, certain compounds, andespecially A0435, also demonstrated antiviral activity in a liveinfection mammalian model of influenza A.

Various objects, features, aspects and advantages of the presentinvention will become more apparent from the following detaileddescription of preferred embodiments of the invention.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 is a schematic of an Influenza A reporter assay construct.

FIG. 2 is a graph indicating requirements of components in a luciferaseassay.

FIG. 3 is a graph depicting exemplary results for enhancement ofexpression in a luciferase assay.

FIG. 4A is a schematic of raw data from a high-throughput screendemonstrating specific inhibition of the reporter system by an exemplarycompound, FIG. 4B depicts the structure of the exemplary compound, andFIG. 4C is a graph illustrating dose response of the reporter system tothe exemplary compound.

FIG. 5A depicts the structure of another exemplary compound, and FIG. 5Bis a graph illustrating dose response of the reporter system to theexemplary compound of FIG. 5A.

FIG. 6A is a photograph of a hemagglutination assay using an exemplarycompound, and FIG. 6B is a photograph illustrating the dose response forthe exemplary compound in the same assay.

FIG. 7A and 7B are photographs illustrating inhibition of viralpropagation in selected cells using an exemplary compound.

FIG. 8A-8C are photographs illustrating inhibition of cytopathic effectsin selected cells by an exemplary compound.

FIG. 9A and 9B are graphs illustrating cytotoxic activity in selectedcells using an exemplary compound.

FIG. 10 is a graph illustrating increase in survival following liveinfection using an exemplary compound.

DETAILED DESCRIPTION

Based on a newly developed ultra-sensitive cell based assay utilizing anRdRP-based reporter system, several compounds were discovered (e.g.,A0435 and A0439) with significant anti-viral activity against anapparently conserved viral target (most likely the viral replicationand/or gene expression machinery).

To enable high-throughput identification of novel small moleculeinhibitors of RdRP activity using a cell-based assay system, theinventors generated a panel of constructs encoding the influenza RdRPsubunit proteins (PB2, PB 1, and PA and the accessory NP protein) and areporter RNA for expression in mammalian cells, and a typical assaysystem is schematically described in FIG. 1. The construct encoding thereporter RNA was designed to utilize a mouse RNA polymerase I promoterexpression cassette to drive the transcription of an anti-sense RNAencoding firefly luciferase flanked by appropriate viral RNA domains.Transfection of these constructs into mouse B16-F10 cells demonstrates arobust signal in cells transfected with all five plasmids (e.g.,encoding PA, PB 1, PB2, NP, and the RNA polymerase I-driven luciferaseRNA construct), but no detectable expression when any of theseconstituents were removed or in the presence of reporter RNA devoid ofUTR-based promoter elements as illustrated in FIG. 2. A similar approachusing a human expression cassette and a different viral serotype hasbeen previously reported².

In a particularly preferred modification, a sixth construct wassimultaneously included driving the expression of the viralnon-structural 1 (NS 1) protein. NS 1 and NS2 are alternate mRNA spliceisoforms encoded by segment 8 of the influenza A virus. NS 1 performs awide variety of functions during viral infection including regulation ofviral RNA synthesis and enhancing viral protein translation³ while NS2is critical for viral RNA export from the host cell nucleus⁴. Theinventors found that expression of NS 1 resulted in an amplification ofsignal strength by approximately tenfold without altering the background“noise” of the system (FIG. 3) in a kinetic study. The inventors alsofound that the preferred window of time for the addition of potentialinhibitors resides within the first 6 hours following removal oftransfection DNA/liposome complexes (or “lipoplexes”) prior to theappearance of detectable reporter activity. Exemplary data illustratingthe increase in sensitivity

Of course, it should be appreciated that the inventive subject matterneed not be limited to the specific components as shown in the Figuresand description below, but may include one or more modified nucleicacids. For example, the RdRP subunit proteins may be from a differentvirus, and/or may be mutated to reflect drug resistant mutant strains orto confer various further advantages. Similarly, the reported gene neednot be limited to luciferase, but may be any other reported gene orsystem. Thus, the signal may be generated as an optical signal(luminescence, fluorescence, quenching, etc.), as a chemicallyidentifiable signal (e.g., via protease action or antigen production),and/or as a biological signal (e.g., cell death, or phenotypic change).Similarly, the nucleic acids may be at least partially integrated into asingle nucleic acid for transfection, or cells may be transiently orpermanently transfected (as a cell line or transgene) to express theRdRP subunit proteins.

Regardless of the particular configuration, it should be appreciatedthat using such assay system as a biological screen, large and diversechemical libraries can be readily interrogated. As a simultaneouscounter screen, the inventors evaluated the same screened samples in aseparate reporter system utilizing a cell death-activated reporterconstruct to distinguish between compounds that specifically inhibitviral RdRP and those that non-specifically inhibit mammalian genetranscription and/or alternatively activate a common cell death pathwayin human cells where either result could be indicative of undesirabledownstream toxicity.

Using these assays and search criteria, the inventors identified, interalia, small molecule A0435 (see FIG. 4a,b ). Dose titration studies ofA0435 on the assay system demonstrated a 50% inhibitory concentration(IC50) of approximately 3 μM and there was no visible inhibitory impacton the level of constitutive gene expression provided by thecounter-screen assay (see FIG. 4c ). A second, structurally similarcompound, A0439, was also tested in the reporter assay and found to showsimilar inhibition of the reporter system, albeit with an IC50approximating 5 μM (see FIG. 5a,b ) and increased toxicity at higherdoses due to precipitation.

Of course, it should be appreciated that numerous other compounds havinga scaffold that includes a pyrazolopyrimidine (or similar structure asshown in Table 1 below) are also deemed suitable, wherein such scaffoldswill include various substituents as illustrated below. Most preferably,and with particular respect to compounds A0435 and A439, it iscontemplated that the pyrazolopyrimidine core (or alternative scaffold)will include an alkoxyaryl or dialkoxyaryl moiety, which may be furtheroptionally substituted. In such compounds, at least one oxygen atom mayalso be replaced with a primary, secondary, or tertiary amine, or with asulfur or selenium atom. Most typically, the aryl is a phenyl or aheteroaryl (preferably with a nitrogen heteroatom). Likewise, theethylpyridine moiety may be replaced by any alkylheteroaryl oralkylaryl, and one or both of the alkyl moieties at thepyrazolopyrimidine core may be replaced by a substituted alkyl, aheteroaryl, or that the two alkyl groups may form a ring. Remarkably,however, several positions at the scaffold could not be modified withoutconcomitant loss or significant reduction in inhibitory action and/orincrease in toxicity as is readily evident from the compounds listed inTable 1.

Comp. Structure IUPAC Name IC50 A0436

6-ethyl-2-(4-fluorophenyl)-5- methyl-N-(2-(pyridin-2-yl)ethyl)pyrazolo[1,5- a]pyrimidin-7-amine >10 uM (toxic to bothantiviral and counterscreen at 50 uM) A0437

N-(2-(pyridin-2-yl)ethyl)-2- p-tolyl-6,7-dihydro-5H-cyclopenta[d]pyrazolo[1,5- a]pyrimidin-8-amine >50 uM (no observedtoxicity or efficacy in either assay tested) A0438

N-(3,4- dimethoxyphenethyl)-2-(3,4- dimethoxyphenyl)-6-ethyl-5-methylpyrazolo[1,5- a]pyrimidin-7-amine >10 uM (toxic to both antiviraland counterscreen at 50 uM) A0440

2-(3,4-dimethoxyphenyl)-6- ethyl-N-(4-fluorophenethyl)-5-methylpyrazolo[1,5- a]pyrimidin-7-amine >50 uM (no observed toxicityor efficacy in either assay tested) A0441

2-(4-fluorophenyl)-N-(2- (pyridin-2-yl)ethyl)-5,6,7,8-tetrahydropyrazolo[5,1- b]quinazolin-9-amine >10 uM (toxic to bothantiviral and counterscreen at 50 uM) A0442

2-(4-chlorophenyl)-N-(2- (pyridin-2-yl)ethyl)-5,6,7,8-tetrahydropyrazolo[5,1- b]quinazolin-9-amine >10 uM (toxic to bothantiviral and counterscreen at 50 uM) A0443

2-(3,4-dimethoxyphenyl)- 5,6-dimethyl-7-(pyrrolidin-1-yl)pyrazolo[1,5-a]pyrimidine >50 uM (no observed toxicity or efficacy ineither assay tested) A0444

2-(3,4-dimethoxyphenyl)-N- (2-(pyridin-3-yl)ethyl)-6,7- dihydro-5H-cyclopenta[d]pyrazolo[1,5- a]pyrimidin-8-amine >10 uM (toxic to bothantiviral and counterscreen at 50 uM) A0445

6-ethyl-5-methyl-2-(5- methylisoxazol-3-yl)-N-(2- (pyridin-2-yl)ethyl)pyrazolo[1,5- a]pyrimidin-7-amine >50 uM (no observed toxicityor efficacy in either assay tested) A0525

2-(3,5-dimethoxyphenyl)-5- methyl-N-(2- phenylpropyl)pyrazolo[1,5-a]pyrimidin-7-amine >50 uM (no observed toxicity or efficacy in eitherassay tested) A0526

N-(2,5-dimethoxybenzyl)-2- (3,4-dimethoxyphenyl)-6-ethyl-5-methylpyrazolo[1,5- a]pyrimidin-7-amine >50 uM (no observedtoxicity or efficacy in either assay tested) A0527

2-(3,5-dimethoxyphenyl)-6- ethyl-5-methyl-N- phenethylpyrazolo[1,5-a]pyrimidin-7-amine >50 uM (no observed toxicity or efficacy in eitherassay tested) A0528

2-(3,4-dimethoxyphenyl)-N- (2-methylbenzyl)-5- phenylpyrazolo[1,5-a]pyrimidin-7-amine >50 uM (no observed toxicity or efficacy in eitherassay tested) A0529

N-(2-fluorobenzyl)-2-(4- methoxyphenyl)-5,6,7,8- tetrahydropyrazolo[5,1-b]quinazolin-9-amine >50 uM (no observed toxicity or efficacy in eitherassay tested) A0530

N-(benzo[d][1,3]dioxol-5- ylmethyl)-2-(4- methoxyphenyl)-5-methylpyrazolo[1,5- a]pyrimidin-7-amine >50 uM (no observed toxicity orefficacy in either assay tested) A0531

2-(2-(3-fluorophenyl)-5- methylpyrazolo[1,5- a]pyrimidin-7-ylamino)-1-phenylpropane-1,3-diol >50 uM (no observed toxicity or efficacy ineither assay tested) A0532

3-(2-(2-(3-fluorophenyl)-5- methylpyrazolo[1,5-a]pyrimidin-7-ylamino)-1- hydroxyethyl)phenol >50 uM (no observedtoxicity or efficacy in either assay tested) A0547

N-(2-methoxybenzyl)-2-(4- methoxyphenyl)pyrazolo[1,5-a]pyrimidin-7-amine >50 uM (no observed toxicity or efficacy in eitherassay tested) A0548

N-benzyl-2-(4- methoxyphenyl)-5- methylpyrazolo[1,5-a]pyrimidin-7-amine >50 uM (no observed toxicity or efficacy in eitherassay tested) A0549

3-(3,4-dimethoxyphenyl)- 2,5-dimethyl-N-(2- phenylpropyl)pyrazolo[1,5-a]pyrimidin-7-amine >50 uM (no observed toxicity or efficacy in eitherassay tested) A0550

2-(3-(3,4-dimethoxyphenyl)- 2,5-dimethylpyrazolo[1,5-a]pyrimidin-7-yl)-1,2,3,4- tetrahydroisoquinoline >50 uM (no observedtoxicity or efficacy in either assay tested) A0551

7-(benzo[d][1,3]dioxol-5- ylmethylthio)-2-(3,4- dimethoxyphenyl)pyrazolo[1,5-d][1,2,4]triazin-4(5H)-one >50 uM (no observed toxicity or efficacyin either assay tested) A0552

2-(4-ethoxyphenyl)-4-(3- methylbenzylthio)pyrazolo [1,5-a]pyrazine >50uM (no observed toxicity or efficacy in either assay tested) A0553

7-(2-chlorobenzylthio)-2- (3,4- dimethoxyphenyl)pyrazolo[1,5-d][1,2,4]triazin-4(5H)-one >50 uM (no observed toxicity or efficacyin either assay tested)

For example, suitable alternative compounds will have a structureaccording to Formula I

wherein X and Y are independently O, S, or NR, wherein R, R1, R2, R3,R4, and R5 are independently H, optionally substituted lower alkyl,optionally substituted lower alkenyl, or NR1R2, OH, or halogen; andwherein Q is optionally substituted aryl or optionally substitutedheteroaryl. More preferably, X and Y in contemplated compounds areoxygen, and/or R1 and R2 are independently ethyl, methyl, ortrifluoromethyl. It is further generally preferred that R3 and

R4 are independently lower alkyl, and especially methyl and ethyl,respectively. In still further preferred aspects, R5 is lower alkyl (andespecially ethyl), and/or Q is optionally substituted phenyl, oroptionally substituted pyridinyl. Particularly preferred compoundsinclude A0435 and A0439 as shown further below.

To further evaluate the antiviral potential of A0435 and A0439 in vitro,MDCK cells were pre-incubated with indicated concentrations of compoundfor 1 hour prior to the addition of live, MDCK-adapted influenzaA/Puerto Rico/8/34 (H1N1) virus. After an 18-20 hour incubation,supernatants were collected and evaluated for the presence of viralhemagglutinin activity indicative of successful viral replication usinga chicken red blood cell hemagglutination assay. In this type of assay,hemagluttinin activity results in the absence of a characteristic red“button” formed by precipitated red blood cells on the bottom ofU-shaped wells. Interestingly, A0435 demonstrated significant antiviralactivity at concentrations >4 μM while A0439 demonstrated similaractivity at >7.5 μM in accordance with the values observed in thetransfection inhibition experiments discussed above as can be seen fromFIG. 6a,b . To determine if the observed antiviral activity of A0435extended to other viral isolates/serotypes, similar in vitro infectionexperiments were performed using the influenza A/WS/1933 (H1N1) and theH3N2 serotype A/Aichi/2/68 viruses which were also significantlyinhibited by A0435 and the results are shown in FIG. 7a,b ). Of equalimportance to drug development, cells infected with live virusdemonstrated little to no signs of the cytopathic effects characteristicof influenza A infection as is evident from FIG. 8 a,b,c. Consistentwith these results, the inventors found that A0435 is well-tolerated intraditional cellular models of toxicity such as those provided byliver-derived HepG2 cells and primary renal proximal tubule epithelialcells (or RPTEC) over a broad range of concentrations as can be takenfrom FIG. 9 a,b.

Encouraged by these results, the inventors initiated studies to gaugethe antiviral efficacy of A0435 in combating live infection in animalsinfected with twice the lethal dose 50% (2xLD50) of influenza A/PuertoRico/8/34. As demonstrated in FIG. 10, 3/5 animals survived infection atday 7 post-infection in the 3.17 mg/kg dosage group, 2/5 animalssurvived at the 1 mg/kg dose, and 0/5 animals survived when injectedwith vehicle only (1× PBS, 3% W/V mouse serum albumin).

Consequently, contemplated compounds include all those that can beidentified in an inhibition assay as exemplarily shown in FIG. 1. Mostpreferably, such compounds will have an IC50 of equal or less than 10μM, even more preferably of equal or less than 1 μM, and most preferablyof equal or less than 100 nM, and will have no apparent toxicity at theIC50 as measured above. Thus, a method of identifying contemplatedcompounds will include a step in which the assay system of FIG. 1 isemployed to screen a compound library for inhibitory compounds. Oncecandidate compounds (typically having IC50 of equal or less than 10 μM)are identified, such compounds can be further modified to ascertain SARand to produce compounds with higher potency, reduced toxicity, and/orincreased bioavailability.

Furthermore it should be noted that the compounds contemplated hereinmay be prepared as prodrugs. The term “prodrug” as used herein refers toa modification of contemplated compounds, wherein the modified compoundexhibits less pharmacological activity (as compared to the modifiedcompound) and wherein the modified compound is converted within a targetcell (e.g., B-cell) or target organ/anatomic structure (e.g., joint)back into the modified form. For example, conversion of contemplatedcompounds into prodrugs may be useful where the active drug is too toxicfor safe systemic administration, or where the contemplated compound ispoorly absorbed by the digestive tract or other compartment or cell, orwhere the body breaks down the contemplated compound before reaching itstarget. Thus, it should be recognized that the compounds according tothe inventive subject matter can be modified in numerous manners, andespecially preferred modifications include those that improve one ormore pharmacokinetic and/or pharmacodynamic parameter. For example, oneor more substituents may be added or replaced to achieve a higher AUC inserum.

On the other hand, and especially where increased solubility is desired,hydrophilic groups may be added. Still further, where contemplatedcompounds contain one or more bonds that can be hydrolyzed (or otherwisecleaved), reaction products are also expressly contemplated. Exemplarysuitable protocols for conversion of contemplated compounds into thecorresponding prodrug form can be found in “Prodrugs (Drugs and thePharmaceutical Sciences: a Series of Textbooks and Monographs)” byKenneth B. Sloan (ISBN: 0824786297), and “Hydrolysis in Drug and ProdrugMetabolism: Chemistry, Biochemistry, and Enzymology” by Bernard Testa,Joachim M. Mayer (ISBN: 390639025X), both of which are incorporated byreference herein. Moreover, especially where contemplated compounds havea higher activity when the compound is metabolized (e.g., hydrolyzed,hydroxylated, glucuronidated, etc.), it should be appreciated thatmetabolites of contemplated compounds are also expressly contemplatedherein.

Additionally, it is contemplated that contemplated compounds may becombined (in vivo or in a pharmaceutical formulation or administrationregimen) with at least one other pharmaceutically active ingredient, andespecially contemplated other ingredients include various antiviraldrugs, various immunomodulatory drugs, and/or anti-inflammatory drugs(e.g., steroids and NSAIDS), etc. Concentrations of secondpharmaceutically active ingredients are typically at or preferably belowthose recommended for stand-alone administration, however, higherconcentrations are also deemed suitable for use herein.

Therefore, contemplated pharmaceutical compositions will especiallyinclude those in which contemplated compounds (and additionalpharmaceutically active ingredients) are provided with a suitablecarrier, wherein contemplated compounds are preferably present at aconcentration effective to reduce viral propagation in an organismand/or target organ to a degree effective to reduce and more preferablyto treat signs and symptoms of a disease associated with the viralinfection. Viewed from a different perspective, contemplated compoundsare present in a composition in an amount effective to treat a viralinfection, and especially a viral infection with an RNA virus (andparticularly influenza virus).

For example, virus infections suitable for treatment with contemplatedcompounds (and especially A0435/A0439) are those produced by infectionwith an RNA virus (and especially a negative stranded RNA virus), andparticularly those viruses bearing the closest resemblance to influenzaA. Thus, contemplated viruses include influenza B (which has beenconfirmed by the inventors as being inhibitable by A0435), and influenzavirus C. Phylogenetically related additional viruses suitable fortreatment with contemplated compounds include mononegavirales familywhich includes paramyxoviridae [including Newcastle disease virus;Hendra virus; Nipah virus; rinderpest virus; measles virus; Sendaivirus; bovine parainfluenza virus 3; human parainfluenza viruses 1 and3; mumps virus; parainfluenza viruses 2, 4a, and 4b; metapneumovirus;respiratory syncytial virus], rhabdoviridae [including the mammalianinfective vesicular stomatitis virus and rabies virus; the plantinfective Strawberry crinkle cytorhabdovirus, lettuce necrotic yellowsvirus, Cynodon chlorotic streak virus, Maize mosaic virus, Northerncereal mosaic virus, Orchid fleck virus, Rice yellow stunt virus,Sonchus yellows net virus, and Taro vein chlorosis virus; the fishinfective Hirame rhabdovirus, infectious hematopoietic necrosis virus,viral hemorrhagic septicemia virus, and Snakehead virus as well asbovine ephemeral fever virus and Adelaide River virus]; the filoviridae[including the hemorrhagic ebolavirus and Marburg viruses] andbornavirus. While the inventors do not have actual data in support ofthese viruses, it should be noted that an RSV-based expression systemcan be used to determine suitability of these viruses, and that suchsystem can be prepared by the PHOSITA without undue experimentation.

Depending on the particular use and structure, it is thereforecontemplated that the compounds according to the inventive subjectmatter are present in the composition in an amount between 1 microgramto 1000 milligram, more typically between 10 microgram to 500 milligram,and most typically between 50 microgram to 500 milligram per singledosage unit. Thus, preferred concentrations of contemplated compounds invivo or in vitro will generally be between 0.1 nM and 500 microM, moretypically between 50 nM and 400 microM, and most typically between 100nM and 200 microM.

Furthermore, it should be recognized that all formulations are deemedsuitable for use herein and especially include oral and parenteralformulations. For example, for oral administration, contemplatedcompositions may be in the form of a tablet, capsule, suspension, orliquid. The pharmaceutical composition is preferably made in the form ofa dosage unit containing a particular amount of the active ingredient.Examples of such dosage units are tablets or capsules. The activeingredient may also be administered by injection as a compositionwherein, for example, saline, dextrose or water may be used as asuitable carrier. In especially preferred aspects, it is contemplatedthat the formulation is suitable for topical administration,administration via aerosol, and for intrathecal administration.Consequently, especially suitable formulations may be sterile aqueoussolutions for topical spray or drop administration, or application as atincture. Alternatively, suitable topical formulations include creams,ointments, foams, lotions, emulsions, etc. Furthermore, where thecompound is formulated for intrathecal administration (e.g., in thetreatment of spinal cord injury), it is preferred that the compound isprepared as an injectable solution, suspension, or emulsion. In stillfurther contemplated formulations, contemplated compounds may beformulated for aerosol delivery (e.g., micropowderized, coated onto adispersible carrier, dissolved in atomizable solvent, etc.)

It should be appreciated that the choice of the particular formulationand carrier will at least in part depend on the specific use and type ofcompound. There are numerous manners of drug formulation known in theart, and all of those are deemed suitable for use herein (see e.g.,Pharmaceutical Preformulation and Formulation: A Practical Guide fromCandidate Drug Selection to Commercial Dosage Form by Mark Gibson;Informa HealthCare, ISBN: 1574911201; or Advanced Drug FormulationDesign to Optimize Therapeutic Outcomes by Robert O. Williams, David R.Taft, and Jason T. McConville; Informa HealthCare; ISBN: 1420043870).

The amount of therapeutically active compound that is administered andthe dosage regimen for treating a disease condition with the compoundsand/or compositions of this invention depends on a variety of factors,including the age, weight, sex and medical condition of the subject, theseverity of the disease, the route and frequency of administration, andthe particular compound employed, and thus may vary widely. However,especially suitable quantities are provided above, and may thereforeallow for a daily dose of about 0.001 (or even less) to 100 mg/kg bodyweight, preferably between about 0.01 and about 50 mg/kg body weight andmost preferably from about 0.1 to 20 mg/kg body weight. Typically, adaily dose can be administered in one to four doses per day.

For therapeutic or prophylactic purposes, contemplated compounds areordinarily combined with one or more excipients appropriate to theindicated route of administration. If administered per os, the compoundsmay be admixed with lactose, sucrose, starch powder, cellulose esters ofalkanoic acids, cellulose alkyl esters, talc, stearic acid, magnesiumstearate, magnesium oxide, sodium and calcium salts of phosphoric andsulfuric acids, gelatin, acacia gum, sodium alginate,polyvinylpyrrolidone, and/or polyvinyl alcohol, and then tableted orencapsulated for convenient administration. Such capsules or tablets maycontain a controlled-release formulation as may be provided in adispersion of active compound in hydroxypropyl-methyl cellulose.Formulations for parenteral administration may be in the form of aqueousor non-aqueous isotonic sterile injection solutions or suspensions.These solutions and suspensions may be prepared from sterile powders orgranules having one or more of the carriers or diluents mentioned foruse in the formulations for oral administration. The compounds may bedissolved in water, polyethylene glycol, propylene glycol, ethanol, cornoil, cottonseed oil, peanut oil, sesame oil, benzyl alcohol, sodiumchloride, and/or various buffers. Other excipients and modes ofadministration are well and widely known in the pharmaceutical art.

Materials and Methods:

Cell-Based Reporter Assays: To identify inhibitors of RdRP, theinventors engineered a mouse cell-based assay system based on thebiology of the virus. To create this system, the viral genes encodingPA, PB 1, PB2, NP, and NS 1 were amplified by reversetranscriptase-polymerase chain reaction (or RT-PCR) of a influenzaA/Puerto Rico/8/34 viral cDNA template using gene-specificoligonucleotides. Resulting PCR products were subsequently cloned into amammalian expression vector (pVAX) utilizing an RNA polymerase IIexpression cassette and the sequences of the inserts were verified byDNA sequencing. To generate the RNA polymerase I-dependent expressioncassette, an RNA polymerase I promoter sequence derived from the 255 bpsequence upstream of the mouse 45S rRNA transcription start site waslinked to a multiple cloning site followed by a 33 bp RNA polymerase Itermination sequence was generated by PCR using overlappingoligonucleotides and cloned into pBluescript in a similar manner topublished reports¹². This construct, called pPolI, was then digestedwithin the multiple cloning site and directionally ligated to a5′UTR/luciferase/3′UTR hence generating pPolI-Luc. The pPolI-Luc-DelUTR(i.e. with deleted UTRs) and pPolI-GFP (which possesses UTRs but encodesthe green fluorescence protein instead of luciferase) constructs weregenerated in an analogous fashion.

Transfections were performed using mouse B16-F10 melanoma cells and acommercially available transfection reagent per the manufacturer'ssuggestions to confirm the system's activity. Briefly, 2 μg of plasmid(e.g. 400 ng of each of constructs encoding PA, PB1, PB2, NP, andpPolI-Luc) were complexed with 15 μL of reagent prior to addition tologarithmically dividing melanoma cells. Transfection complexes wereremoved after four hours and unless otherwise noted, luciferase activitywas assayed 20 hours post-transfection. Experiments involving NS 1 wereperformed in an analogous manner wherein the total amount of plasmid DNAremained fixed at 2 μg but only 333 ng of each plasmid was used due tothe need for six plasmids.

Viruses and In Vitro Viral Propagation: Influenza A/PuertoRico/8/34(H1N1), A/WSN/1933(H1N1), and A/Aichi/2/68(H3N2) werepropagated in canine MDCK cells. On the day preceding infection, MDCKcells were plated in Dulbecco's modified eagle media (D-MEM)supplemented with 10% V/V fetal calf serum and incubated at 37 C at 5%CO2 at densities that would result in 70-90% confluency on the followingday. On the day of infection, cells are washed 3 times using completeDMEM/7.5% BSA/25 mM HEPES/(2 ug/mL) TPCK-trypsin prior to receivingvirus dilutions.

A0435 Inhibition Studies: For studies involving the B16-F10 transfectionsystem, cells were allowed to recover for 5 hours following the removalof DNA/lipid complexes prior to the addition of indicated amounts ofA0435. Luciferase expression was determined 14 hours later. For studiesinvolving inhibition of viral proliferation, cells received indicatedamounts of A0435 thirty minutes prior to the addition of viruspreparations which were allowed to infect for 2 hours prior to beingremoved and the recipient cells washed of non-bound virus and the mediareplaced with corresponding amounts of A0435.

Hemagglutination Assays: Hemagglutination assays were performed asfollows. Briefly, 18-20 hours after initial infection, supernatants wereincubated with 0.50% chicken red blood cells at a 1:1 ratio (V/V) unlessotherwise noted in U-bottom wells and reactions were monitoredphotographically.

In Vivo Survival Studies: Groups of 5 Balb/C mice (age/gender) wereweighed prior to the start of study and injected intravenously at thebase of the tail with formulations containing A0435 at doses of 3.17, 1,or 0 mg/kg in phosphate buffered saline containing 3% w/v mouse serumalbumin. Four hours later, these mice were challenged intranasally with2xLD50 of influenza A/Puerto Rico/8/34 under anesthesia. Identical dosesof A0435 were administered 24 and 48 hours after the initial doseadministration and animal weights were monitored daily. Survivinganimals were defined as those who maintained 70% or more of theirstarting weight.

Related Art

1) Fields Virology 5th edition. Edited by David M Knipe and Peter MHowley, Lippincott-Raven, Philadelphia, USA, 2007.

2) Lutz A, Dyall J, Olivo P D, Pekosz A. Virus-inducible reporter genesas a tool for detecting and quantifying influenza A virus replication. JVirol Methods. 2005 June; 126(1-2):13-20.

3) Hale B G, Randall R E, Oran J, Jackson D. The multifunctional NS1protein of influenza A viruses. J Gen Virol. 2008 October; 89(Pt10):2359-76.

4) Robb N C, Smith M, Vreede F T, Fodor E. NS2/NEP protein regulatestranscription and replication of the influenza virus RNA genome. J GenVirol. 2009 June; 90(Pt 6):1398-407.

5) “Update on oseltamivir resistance to influenza H1N1 (2009) viruses”.World Health Organization (WHO). Dec. 15, 2010.

6) Kiso M, Mitamura K; Sakaitagawa Y, Shiraishi K, Kawakami C, Kimura K,Hayden F, Sugaya N, Kawaoka Y. (2004). Resistant influenza A viruses inchildren treated with oseltamivir: descriptive study. The Lancet 364:759-765

7) Le M, Kiso M, Someya K, Sakai T, Nguyen H, Nguyen H, Pham D, Ngyen H,Yamada S, Muramoto Y, Horimoto T, Takada A, Goto H, Suzuki T, Suzuki Y,Kawaoka Y. Avian flu: isolation of drug-resistant H5N1 virus. Nature2005, 437(7062): 1108

8) Dharan N J, Infections with oseltamivir-resistant influenza A(H1N1)virus in the United States. JAMA, 2009. 301(10): p. 1034-41.

9) Gubareva L V, Matrosovich M N, Brenner M K, Bethell R C, Webster R G.Evidence for zanamivir resistance in an immunocompromised child infectedwith influenza B virus. J Infect Dis. 1998 November; 178(5):1257-62.

10) http://www.cdc.gov/flu/weekly/weeklyarchives2008-2009/weekly35.htm

11) Sheu T G, Fry A M, Garten R J, Deyde V M, Shwe T, Bullion L, PeeblesP J, Li Y, Klimov A I, Gubareva L V. Dual resistance to adamantanes andoseltamivir among seasonal influenza A(H1N1) viruses: 2008-2010. JInfect Dis. 2011 Jan. 1; 203(1):13-7.

12) Neumann G, Zobel A, Hobom G. RNA polymerase I-mediated expression ofinfluenza viral RNA molecules. Virology. 1994 July; 202(1):477-9.

Thus, specific embodiments and applications of small molecule inhibitorsof influenza A RNA-dependent RNA polymerase have been disclosed. Itshould be apparent, however, to those skilled in the art that many moremodifications besides those already described are possible withoutdeparting from the inventive concepts herein. The inventive subjectmatter, therefore, is not to be restricted except in the spirit of theappended claims.

What is claimed is:
 1. A pharmaceutical composition comprising: acompound according to Formula I in combination with a pharmaceuticallyacceptable carrier

wherein R₁ and R₂ are independently H, halogen or alkoxy group; whereinR₃ and R₄ are independently H, lower alkyl, or form together a 5- or6-membered cycloalkyl ring; wherein R₅ is H, lower alkyl; wherein R₆ isaryl or heteroaryl, optionally substituted with a lower alkyl orhalogen; wherein the alkyl, the aryl, and the heteroaryl areindependently optionally substituted with halogen, alkyl, alkoxy, orhydroxy; and wherein the compound is present in the pharmaceuticalcomposition in an amount effective to reduce viral propagation of avirus in a patient when the compound is administered to the patient inneed thereof, and wherein the virus belongs to the family offiloviridae.
 2. The pharmaceutical composition of claim 1 wherein R₂ isF or Cl.
 3. The pharmaceutical composition of claim 1 or claim 2 whereinR₁ and R₂ are independently ethoxy, methoxy, or trifluoromethoxy.
 4. Thepharmaceutical composition of claim 1 or claim 2 wherein R₃ and R₄ formtogether a 5- or 6-membered cycloalkyl ring.
 5. The pharmaceuticalcomposition of claim 1 wherein R₅ is —(CH₂)₂—.
 6. The pharmaceuticalcomposition of claim 1 wherein R₆ is pyridinyl or phenyl.
 7. Thepharmaceutical composition of claim 1 wherein R₆ is substituted withmethyl.
 8. The pharmaceutical composition of claim 1 wherein thecompound is A0435(2-(3,4-dimethoxyphenyl)-6-ethyl-5-methyl-N-[2(pyridin-2-yl)ethyl]pyrazolo[1,5-a]pyrimidin-7-amine).9. The pharmaceutical composition of claim 1 wherein the compound isA0439(2-(3,4-dimethoxyphenyl)-6-ethyl-5-methyl-N-└2(2-methylphenyl)ethyl┘pyrazolo└1,5-a┘pyrimidin-7-amine).10. The pharmaceutical composition of claim 1 wherein the virus is anEbolavirus.
 11. The pharmaceutical composition of claim 1 wherein thevirus is a Marburg virus.
 12. A method of treating a viral infection ina patient comprising a step of administering the pharmaceuticalcomposition of claim 1 to a patient under a protocol effective to reduceviral propagation of an RNA virus in the patient.
 13. The method ofclaim 12 wherein the virus is an Ebolavirus.
 14. The method of claim 12wherein the virus is a Marburg virus.